A maximum likelihood method for estimating genome length using genetic linkage data.
A maximum likelihood method for estimating genome length using genetic linkage data.
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DOI：
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发表时间：
1991-05
期刊：
影响因子：
3.3
通讯作者：
A. Chakravarti;Laura K. Lasher;Jillian E. Reefer
中科院分区：
文献类型：
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作者：
A. Chakravarti;Laura K. Lasher;Jillian E. Reefer
基因组的遗传长度，以摩尔根或厘摩为单位，是生物体的一个基本特征。我们提出一种极大似然法，用于从回交连锁实验所研究的标记基因座对之间的重组体和非重组体数量来估计这一数量，假定无干扰且染色体长度相等。这种方法能够计算估计值的标准差以及包含该估计值的置信区间。我们进行了计算机模拟，以评估和比较极大似然法和先前提出的矩估计法的准确性。具体而言，我们研究了减数分裂次数、标记基因座数量以及单个染色体遗传长度的变化对估计值的影响。我们还研究了在将两个有部分共同标记基因座的独立连锁研究结果合并时出现的缺失数据的影响。与矩估计法不同，极大似然估计量对分析过程中所做假设的违反相对不敏感，是首选方法。通过应用于剑尾鱼的部分连锁数据对各种方法进行了比较。
The genetic length of a genome, in units of Morgans or centimorgans, is a fundamental characteristic of an organism. We propose a maximum likelihood method for estimating this quantity from counts of recombinants and nonrecombinants between marker locus pairs studied from a backcross linkage experiment, assuming no interference and equal chromosome lengths. This method allows the calculation of the standard deviation of the estimate and a confidence interval containing the estimate. Computer simulations have been performed to evaluate and compare the accuracy of the maximum likelihood method and a previously suggested method-of-moments estimator. Specifically, we have investigated the effects of the number of meioses, the number of marker loci, and variation in the genetic lengths of individual chromosomes on the estimate. The effect of missing data, obtained when the results of two separate linkage studies with a fraction of marker loci in common are pooled, is also investigated. The maximum likelihood estimator, in contrast to the method-of-moments estimator, is relatively insensitive to violation of the assumptions made during analysis and is the method of choice. The various methods are compared by application to partial linkage data from Xiphophorus.